Replaced dashes with underscores in database_import_scripts

EBI-Metagenomics · Nov 19, 2024 · b0a826c · b0a826c
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commit b0a826c
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Showing 13 changed files with 5 additions and 5 deletions.
diff --git a/...pts/rnacentral/calculate_model_lengths.py → ...pts/rnacentral/calculate_model_lengths.py b/...pts/rnacentral/calculate_model_lengths.py → ...pts/rnacentral/calculate_model_lengths.py
diff --git a/...ts/rnacentral/generate_rnacentral_json.py → ...ts/rnacentral/generate_rnacentral_json.py b/...ts/rnacentral/generate_rnacentral_json.py → ...ts/rnacentral/generate_rnacentral_json.py
diff --git a/...scripts/rnacentral/rfam_model_lengths.txt → ...scripts/rnacentral/rfam_model_lengths.txt b/...scripts/rnacentral/rfam_model_lengths.txt → ...scripts/rnacentral/rfam_model_lengths.txt
diff --git a/...ts/rnacentral/rfam_model_lengths_14.9.txt → ...ts/rnacentral/rfam_model_lengths_14.9.txt b/...ts/rnacentral/rfam_model_lengths_14.9.txt → ...ts/rnacentral/rfam_model_lengths_14.9.txt
diff --git a/...tabase-import-scripts/uniprot/__init__.py → ...tabase_import_scripts/uniprot/__init__.py b/...tabase-import-scripts/uniprot/__init__.py → ...tabase_import_scripts/uniprot/__init__.py
diff --git a/...ase-import-scripts/uniprot/convert_gbk.py → ...ase_import_scripts/uniprot/convert_gbk.py b/...ase-import-scripts/uniprot/convert_gbk.py → ...ase_import_scripts/uniprot/convert_gbk.py
diff --git a/...ipts/uniprot/generate_uniprot_metadata.py → ...ipts/uniprot/generate_uniprot_metadata.py b/...ipts/uniprot/generate_uniprot_metadata.py → ...ipts/uniprot/generate_uniprot_metadata.py
diff --git a/...pts/uniprot/gtdb_to_ncbi_majority_vote.py → ...pts/uniprot/gtdb_to_ncbi_majority_vote.py b/...pts/uniprot/gtdb_to_ncbi_majority_vote.py → ...pts/uniprot/gtdb_to_ncbi_majority_vote.py
diff --git a/.../uniprot/gtdb_to_ncbi_majority_vote_v2.py → .../uniprot/gtdb_to_ncbi_majority_vote_v2.py b/.../uniprot/gtdb_to_ncbi_majority_vote_v2.py → .../uniprot/gtdb_to_ncbi_majority_vote_v2.py
diff --git a/...niprot/preprocess_taxonomy_for_uniprot.py → ...niprot/preprocess_taxonomy_for_uniprot.py b/...niprot/preprocess_taxonomy_for_uniprot.py → ...niprot/preprocess_taxonomy_for_uniprot.py
diff --git a/...t-scripts/uniprot/uniprot_sanity_check.py → ...t_scripts/uniprot/uniprot_sanity_check.py b/...t-scripts/uniprot/uniprot_sanity_check.py → ...t_scripts/uniprot/uniprot_sanity_check.py
diff --git a/helpers/file_organiser.sh b/helpers/file_organiser.sh
@@ -51,8 +51,8 @@ function GenerateRNACentralJSON {
 
     echo "Running JSON generation"
     mitload miniconda && conda activate pybase
-    rna_cmd="python3 /nfs/production/rdf/metagenomics/pipelines/prod/genomes-pipeline/helpers/database-import-scripts/rnacentral/generate_rnacentral_json.py \
-    -r /nfs/production/rdf/metagenomics/pipelines/prod/genomes-pipeline/helpers/database-import-scripts/rnacentral/rfam_model_lengths_14.9.txt \
+    rna_cmd="python3 /nfs/production/rdf/metagenomics/pipelines/prod/genomes-pipeline/helpers/database_import_scripts/rnacentral/generate_rnacentral_json.py \
+    -r /nfs/production/rdf/metagenomics/pipelines/prod/genomes-pipeline/helpers/database_import_scripts/rnacentral/rfam_model_lengths_14.9.txt \
     -m "${RESULTS_PATH}/genomes-all_metadata.tsv" -o "${RESULTS_PATH}/additional_data/rnacentral/${CATALOGUE_FOLDER}-rnacentral.json" \
     -d "${RESULTS_PATH}/additional_data/ncrna_deoverlapped_species_reps/" -g "${RESULTS_PATH}/additional_data/rnacentral/GFFs/ "\
      -f "${RESULTS_PATH}/additional_data/mgyg_genomes/""
@@ -134,7 +134,7 @@ function GenerateUniprotFiles {
     fi
 
     mitload miniconda && conda activate pybase
-    python3 /nfs/production/rdf/metagenomics/pipelines/prod/genomes-pipeline/helpers/database-import-scripts/uniprot/preprocess_taxonomy_for_uniprot.py \
+    python3 /nfs/production/rdf/metagenomics/pipelines/prod/genomes-pipeline/helpers/database_import_scripts/uniprot/preprocess_taxonomy_for_uniprot.py \
     -g ${RESULTS_PATH}/additional_data/gtdbtk_results/ -r "r214" -v "2" \
     -m ${RESULTS_PATH}/ftp/genomes-all_metadata.tsv --species-level-taxonomy -t 4 \
     -o ${RESULTS_PATH}/additional_data/uniprot/preprocessed_taxonomy.tsv

diff --git a/tests/scripts/test_generate_rnacentral_json.py b/tests/scripts/test_generate_rnacentral_json.py
@@ -6,10 +6,10 @@
 from pathlib import Path
 
 script_dir = Path(__file__).resolve().parent
-rnacentral_dir = script_dir / '../../helpers/database-import-scripts/rnacentral'
+rnacentral_dir = script_dir / '../../helpers/database_import_scripts/rnacentral'
 rnacentral_dir = rnacentral_dir.resolve()
 
-generate_json = importlib.import_module("helpers.database-import-scripts.rnacentral.generate_rnacentral_json")
+generate_json = importlib.import_module("helpers.database_import_scripts.rnacentral.generate_rnacentral_json")
 generate_metadata_dict = generate_json.generate_metadata_dict
 get_good_hits = generate_json.get_good_hits
 load_rfam = generate_json.load_rfam